1. Avogadro Scale Engineering & Fabricational Complexity
MIT
Avogadro Scale Engineering &
Fabricational Complexity
NSF-CBA Program Review
MIT Cambridge, MA October 12, 2006
Molecular Machine (Jacobson) Group

2. Complexity vs. Size m 10-10 10-5 10-9 10-7 10-6 10-8 10-4 10-3 10-2
red blood cell
~5 m (SEM)
diatom
30 m
Simple molecules
<1nm
DNA
proteins nm
bacteria
1 m m
10-10
10-5
10-9
10-7
10-6
10-8
10-4
10-3
10-2
SOI transistor
width 0.12m
Semiconductor
Nanocrystal
~1 nm
Circuit design
Copper wiring
width 0.1m
Nanotube Transistor
(Dekker)
IBM PowerPC 750TM Microprocessor
7.56mm×8.799mm
6.35×106 transistors

3. Chemical Synthesis (Solid Phase Synthesis)
DNA Synthesis
Chemical Synthesis (Solid Phase Synthesis)
Biological Synthesis (Error Correcting Polymerase)
Error Rate:
1: 102
300 Seconds
Per step
Error Rate:
1: 106
100 Steps per second
3'-5' proofreading exonuclease
Beese et al. (1993), Science, 260,

4. Resources for Exponential Scaling
Resources which increase the complexity of a system exponentially with a linear addition of resources
1] Quantum Phase Space
2] Error Correcting Fabrication
3] Fault Tolerant Hardware Architectures
4] Fault Tolerant Software or Codes

5. Complexity Per Unit Cost
[I]Non Error Correcting: A G T C
[II] Triply Error Correcting: A G T C A G T C A G T C
P = 0.9
n = 300
P = 0.85 n n p

6. Deinococcus radiodurans
(3.2 Mb, Copies of Genome )
D. radiodurans
1.75 million rads, 0 h
D. radiodurans
1.75 million rads, 24 h
Uniformed Services University of the Health
[Nature Biotechnology 18, (January 2000)]
D. radiodurans: 1.7 Million Rads (17kGy) – 200 DS breaks
E. coli: 25 Thousand Rads – 2 or 3 DS breaks
photos provided by David Schwartz (University of Wisconsin, Madison)]

7. Synthetic Self Replication -Building a Fab for Biology-
BioFAB
-Building a Fab for Biology-
“Robotics: Self-replication from random parts.”
Nature (2005), 437(7059), 636
Griffith, S. et. al.
Carr, P. et.al. .. “ Protein-mediated error correction for de novo DNA synthesis.” Nucleic Acids Research (2004), 32(20), e162/1-e162/9.
Molecular Machines Group-MIT
Faculty
Joseph Jacobson
Graduate Students
Brian Chow
David Kong
Chris Emig
Jae Bum Joo
Sam Hwang
Kimin Jun
Undergrad
Bram Sterling,Lu Chen,Ekatarina Pak,Michael Oh
Research Scientists and Post Docs
Peter Carr
Sangjun Moon
Alumni
Saul Griffith
Jason Park
Air inlets
Crushers
Ganglion
Multiple Visual sensors
Muscles
Pincers
Sensory receptors
Stridulatory pegs
Wings